Align Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase; Pyr2C/Pip2C reductase; N-methyl-L-amino acid dehydrogenase; EC 1.5.1.21; EC 1.4.1.17 (characterized)
to candidate SMa0265 SMa0265 dehydrogenase
Query= SwissProt::Q4U331 (343 letters) >FitnessBrowser__Smeli:SMa0265 Length = 334 Score = 145 bits (366), Expect = 1e-39 Identities = 111/322 (34%), Positives = 147/322 (45%), Gaps = 21/322 (6%) Query: 30 GTSPEVADVLAENCASAQRDGSHSHGIFRIPGYLSSLASGWVDGKAVPVVEDVG----AA 85 G + A + A A+ G SHG+ R+P LS L G + P G A+ Sbjct: 20 GVPADSARLQANLLLEAELRGLPSHGLQRLPLLLSRLDKGLAN----PTTRGNGTWRRAS 75 Query: 86 FVRVDACNGFAQPALAAARSLLIDKARSAGVAILAIRGSHHFAALWPDVEPFAEQGLVAL 145 F+ VD G + A + + G+AI AIR ++H L E A GL+ + Sbjct: 76 FLSVDGERGLGPVVMMDAMRVTRRILKETGLAIAAIRNANHMGMLAYYAEAAARDGLIGI 135 Query: 146 SMVNSMTCVVPHGARQPLFGTNPIAFGAPRAGGEPIVFDLATSAIAHGDVQIAAREGRLL 205 M S V P G Q L GTNP+A G P A G P V DLATS ++ G + A G + Sbjct: 136 VMSTSEALVHPFGGTQALIGTNPVAIGIP-AAGHPFVLDLATSIVSMGKINNHAMRGLAI 194 Query: 206 PAGMGVDRDGLPTQEPRAILDGGALLPFGGHKGSALSMMVELLAAGLTGGNFSFEFDWSK 265 P G VDRDG T +P A GA+ PFG KG L + +ELL A L G N + + + + Sbjct: 195 PPGWAVDRDGRATTDPHA-AQAGAIAPFGDAKGYGLGLAIELLVAALAGSNLAPDVNGTL 253 Query: 266 ---HPGAQTPWTGQLLIVIDPDKGAGQHFAQRSE----ELVRQLHGVGQERLPGDRRYLE 318 HP + G LLI+IDP GAG A + L R L +PGD Sbjct: 254 DDIHPANK----GDLLILIDPSAGAGSIPALAAYLDRLRLSRPLDPTQPVAIPGDGARAR 309 Query: 319 RARSMAHGIVIAQADLERLQEL 340 RA + GI + Q + L L Sbjct: 310 RAAAAKTGIELPQPLFDHLTAL 331 Lambda K H 0.320 0.137 0.412 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 325 Number of extensions: 24 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 343 Length of database: 334 Length adjustment: 28 Effective length of query: 315 Effective length of database: 306 Effective search space: 96390 Effective search space used: 96390 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory